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Water pooled onto the marble floors of the Oculus during a drenching downpour that swamped the city Friday, with liquid appearing to rain down from above.

The pricey structure stretches two stories below ground, with a mezzanine overlooking an open concourse.

The roof is fine, the Port Authority insisted Saturday — instead pinning the blame on nearby construction which left corridors on the edges of the Oculus vulnerable to flooding.

Much of the rainwater barreled through 3 World Trade Center, a still unfinished Larry Silverstein-owned tower south of the Oculus, the Port Authority said.

The water flowed into an underground passageway connecting the tower to the oval-shaped hall and streamed from the mezzanine-level corridors onto the bottom floor of the Oculus.

“Somehow water is getting into open areas of World Trade Center 3, leaking into Tower 3,” said Port Authority spokesman Steve Coleman.

William Farrington

“Once it leaks into lower levels, all those areas below ground are interconnected. And if you look at the areas of leaks, they’re under the Tower 3 footprint,” he said.

William Farrington

Water also leaked into the Oculus from the east side of the mezzanine near Church Street, from a corridor connecting it to the Fulton Transit Center, but there was no indication it came through the roof, Coleman added.

But a Silverstein spokesman threw cold water on the Port Authority’s theory, and said the developer’s lower Manhattan skyscraper suffered no water damage.

“Anyone who suggests that the water leaking into the Oculus somehow originated at 3 World Trade Center . . . is all wet,” said Silverstein spokesman Bud Perrone. “All of the areas impacted by rainwater are parts of the Hub project, built and operated by the Port Authority.”

The Santiago Calatrava-designed PATH terminal, which also includes a warren of luxury retailers, opened last March after being seven years behind schedule and $2 billion over budget. The architect declined comment.

It has been a rocky first year for the bird-like transit hub.

In February a woman fell to her death from the escalator while reaching for her sister’s hat.

Last week, two men were hurt when the escalator appeared to “buckle,” leaving them with minor injuries.

Weary commuters waded through pools of water as three inches of rain in three hours caused flash flooding throughout the region.

The flooding was so bad, parts of the eastern mezzanine were shuttered Friday afternoon, with buckets and water vacuums at the ready.

“It was almost impossible to walk with all the water in here,” said Carissa Esposito of downtown Brooklyn. “I guess that’s why people were evacuating.”

And Bushwick resident Chris Toscano, 29, said it “felt like it was literally raining indoors.”

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“I was just trying to get home from work a little early, and as soon as I got here, [the weather] felt the same as outside,” he added.

Port Authority construction engineers examined the ground and mezzanine floors of the Oculus on Saturday to see how they could prevent future damage.

Legislators are demanding answers from the Port Authority.

“There should be both a hearing and an investigation into the Port Authority’s spending practices,” said Assemblywoman Nicole Malliotakis, who sits on the Assembly Transportation Committee.

“To spend $4 billion in taxpayer money and have this magnitude of a problem so soon is another example of how this bloated agency continues to be mismanaged,” said Malliotakis, a Republican candidate for mayor.